Complex Queries

        The simple selection queries detailed above can be combined to create complex expressions. The simplest method of combination is a simple comma separating the two parts, which is treated as a logical ``and'', so the final selection must satisfy both parts of the expression. For example: bc=1,rn=(1,10),a=ca will color bonds 1 only for alpha carbons in residues 1-10. Instead of a comma, the C ``and'' operator ``&&'' may also be used to create logical ``and'' constructs. The C ``or'' operator ``||'' is also allowed to create expressions that match one component or the other, e.g. a=ca||a=cb selects atoms named ``CA'' or atoms named ``CB''. Finally, the English words ``and'' and ``or'' are also recognized. If you use the English words, however, they must be separated from the rest of the command by spaces, e.g. r=ala and a=ca. Evaluation of expressions is normally carried out in a left-to right fashion, but curly braces may be used to control the order of operations. The ``&&'' and ``||'' operators have the same precedence, so it is usually a good idea with complex expressions to specify the grouping explicitly.

Examples:

• r=CHARGED&&a=oe1||r=NEUTRAL&&a=ca: this will select only CA atoms from NEUTRAL residues. First, any charged residues are selected, and then all atoms are eliminated which are not OE1. Next, any NEUTRAL residues are added to the selection, so that it now consists of CHARGED OE1's and all NEUTRAL atom. Finally all atoms that are not CA's are eliminated, which leaves only the CA's of the NEUTRAL residues. Clearly, braces should usually be used!
• {r=CHARGED&&a=oe1}||{r=NEUTRAL&&a=ca}: OE1 of CHARGED residues or CA of NEUTRAL residues is selected.
• {r=ala&&{d<5.0&&d<>0}||r=phe}&&a=ca}: the translation is left as an exercise.

Note that the innermost set of braces is evaluated first. Occasionally, when working with a long LIST of items, spock may complain that the list generates too long of an expression. This is because the LIST structure (rn=[1,3,5,7]) is internally translated into an ``OR'' based construct (rn=1||rn=3||rn=5||rn=7). This may occasionally generate a string that is too long for the internal buffers. A work-around for this is to simplify the part of the expression using a subset, and then include the subset as part of the selection scheme. Say the string above was part of a larger expression that proved to be too long. You could use a subdef=temp,rn=[1,3,5,7] and then replace that part of the expression with sub=temp. See § 6.8 for more details on subsets.  

Projection

  The final feature of spock's selection syntax is ``projection''. Currently, the only form of projection is projection to residues. This means that if any atom in a residue is selected, the entire residue gets selected. The syntax for projection is to surround the selection with parentheses and add ->r to the command. For example, bc=3,(q>0)->r will color all bonds in residues that have any charged atom with color 3. There can be more than one selection string in the parentheses: e.g. bc=0,(q>0||d>0)->r, which will hide all bonds for residues which have any atom with a charge or distance property greater than 0. This is a hideously ugly syntax, I know, but it does prove to be quite useful, particularly in conjunction with the ``Projected Command'' option of the Picking menu § 6.9.1.